added pre-qc-failed status filter

[KateSakharova]

Added filtering for not re-trying pre-qc failed assemlies and amplicons

[mberacochea]

Good catch.. not sure if we should rename the analyses QC to PRE-QC

[mberacochea]

This one should go first; it doesn't change how it works—just improves readability

[SandyRogers]

A little manager mixin helper would be nice for building these more readably:

class SelectByStatusManagerMixin:
    STATUS_FIELDNAME = "status"
    
    def filter_by_statuses(self, statuses_to_be_true: List[Union[str, Enum]] = None, statuses_to_be_false: List[Union[str, Enum]] = None):
        """
        Filter queryset by a combination of statuses in the objects status json field.
        """
        filters = {}
        if statuses_true:
            filters = {
                f"{self.STATUS_FIELDNAME}__{must_be}": True
                for must_be in statuses_true
            }
        if statuses_false:
            filters.update({
                f"{self.STATUS_FIELDNAME}__{must_not_be}": True
                for must_not_be in statuses_false
            })
        return super().get_queryset().filter(**filters)

Then we can do class AssemblyManager(SelectByStatusManagerMixin, ENADerivedManager): ...

and select more readably, like

assemblies_worth_trying = study.assemblies_reads.filter_by_statuses(
    statuses_to_be_false=[
        analyses.models.Assembly.AssemblyStates.ASSEMBLY_COMPLETED,
        analyses.models.Assembly.AssemblyStates.ASSEMBLY_BLOCKED,
        analyses.models.Assembly.AssemblyStates.PRE_ASSEMBLY_QC_FAILED,
    ]
).values_list("id", flat=True)

(or maybe better yet include an exclude_by_statuses chainable method on the mixin).

Happy to add this later as it will need a couple of new tests. Just documenting whilst it came to mind!

[SandyRogers]

A little manager mixin helper would be nice for building these more readably:

class SelectByStatusManagerMixin:
    STATUS_FIELDNAME = "status"
    
    def filter_by_statuses(self, statuses_to_be_true: List[Union[str, Enum]] = None, statuses_to_be_false: List[Union[str, Enum]] = None):
        """
        Filter queryset by a combination of statuses in the objects status json field.
        """
        filters = {}
        if statuses_true:
            filters = {
                f"{self.STATUS_FIELDNAME}__{must_be}": True
                for must_be in statuses_true
            }
        if statuses_false:
            filters.update({
                f"{self.STATUS_FIELDNAME}__{must_not_be}": True
                for must_not_be in statuses_false
            })
        return super().get_queryset().filter(**filters)

Then we can do class AssemblyManager(SelectByStatusManagerMixin, ENADerivedManager): ...

and select more readably, like

assemblies_worth_trying = study.assemblies_reads.filter_by_statuses(
    statuses_to_be_false=[
        analyses.models.Assembly.AssemblyStates.ASSEMBLY_COMPLETED,
        analyses.models.Assembly.AssemblyStates.ASSEMBLY_BLOCKED,
        analyses.models.Assembly.AssemblyStates.PRE_ASSEMBLY_QC_FAILED,
    ]
).values_list("id", flat=True)

(or maybe better yet include an exclude_by_statuses chainable method on the mixin).

Happy to add this later as it will need a couple of new tests. Just documenting whilst it came to mind!

[SandyRogers]

@KateSakharova I ended up implementing the suggested SelectByStatusManagerMixin (#24 (comment)) in #28 as I needed to fix another bug with status lookups. You can therefore use that for Assembly state lookups here if you wish

[KateSakharova]

@SandyRogers thank you, I will rebase from your branch!